## skchem.standardizers.chemaxon
Module wrapping ChemAxon Standardizer. Must have standardizer installed and license activated.
skchem.standardizers.chemaxon.ChemAxonStandardizer(config_path=None, keep_failed=False, **kwargs)[source]¶Bases: skchem.base.CLIWrapper, skchem.base.BatchTransformer, skchem.base.Transformer, skchem.filters.base.TransformFilter
ChemAxon Standardizer Wrapper.
| Parameters: | config_path (str) – The path of the config_file. If None, use the default one. |
|---|
Notes
ChemAxon Standardizer must be installed and accessible as standardize from the shell launching the program.
Warning
Must use a unique index (see #31).
Examples
>>> import skchem
>>> std = skchem.standardizers.ChemAxonStandardizer()
>>> m = skchem.Mol.from_smiles('CC.CCC')
>>> print(std.transform(m))
<Mol: CCC>
>>> data = [m, skchem.Mol.from_smiles('C=CO'), skchem.Mol.from_smiles('C[O-]')]
>>> std.transform(data)
0 <Mol: CCC>
1 <Mol: CC=O>
2 <Mol: CO>
Name: structure, dtype: object
>>> will_fail = mol = '''932-97-8
... RDKit 3D
...
... 9 9 0 0 0 0 0 0 0 0999 V2000
... -0.9646 0.0000 0.0032 C 0 0 0 0 0 0 0 0 0 0 0 0
... -0.2894 -1.2163 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0
... -0.2894 1.2163 0.0025 C 0 0 0 0 0 0 0 0 0 0 0 0
... -2.2146 0.0000 -0.0004 N 0 0 0 0 0 0 0 0 0 0 0 0
... 1.0710 -1.2610 0.0002 C 0 0 0 0 0 0 0 0 0 0 0 0
... 1.0710 1.2610 0.0007 C 0 0 0 0 0 0 0 0 0 0 0 0
... -3.3386 0.0000 -0.0037 N 0 0 0 0 0 0 0 0 0 0 0 0
... 1.8248 0.0000 -0.0005 C 0 0 0 0 0 0 0 0 0 0 0 0
... 3.0435 0.0000 -0.0026 O 0 0 0 0 0 0 0 0 0 0 0 0
... 1 2 1 0
... 1 3 1 0
... 1 4 2 3
... 2 5 2 0
... 3 6 2 0
... 4 7 2 0
... 5 8 1 0
... 8 9 2 0
... 6 8 1 0
... M CHG 2 4 1 7 -1
... M END
... '''
>>> will_fail = skchem.Mol.from_molblock(will_fail)
>>> std.transform(will_fail)
nan
>>> data = [will_fail] + data
>>> std.transform(data)
0 None
1 <Mol: CCC>
2 <Mol: CC=O>
3 <Mol: CO>
Name: structure, dtype: object
>>> std.transform_filter(data)
1 <Mol: CCC>
2 <Mol: CC=O>
3 <Mol: CO>
Name: structure, dtype: object
>>> std.keep_failed = True
>>> std.transform(data)
0 <Mol: [N-]=[N+]=C1C=CC(=O)C=C1>
1 <Mol: CCC>
2 <Mol: CC=O>
3 <Mol: CO>
Name: structure, dtype: object
DEFAULT_CONFIG = '/home/docs/checkouts/readthedocs.org/user_builds/scikit-chem/checkouts/latest/skchem/standardizers/default_config.xml'¶columns¶install_hint = ' Install ChemAxon from https://www.chemaxon.com. It requires a license,\n which can be freely obtained for academics. '¶skchem.standardizers.ChemAxonStandardizer(config_path=None, keep_failed=False, **kwargs)[source]¶Bases: skchem.base.CLIWrapper, skchem.base.BatchTransformer, skchem.base.Transformer, skchem.filters.base.TransformFilter
ChemAxon Standardizer Wrapper.
| Parameters: | config_path (str) – The path of the config_file. If None, use the default one. |
|---|
Notes
ChemAxon Standardizer must be installed and accessible as standardize from the shell launching the program.
Warning
Must use a unique index (see #31).
Examples
>>> import skchem
>>> std = skchem.standardizers.ChemAxonStandardizer()
>>> m = skchem.Mol.from_smiles('CC.CCC')
>>> print(std.transform(m))
<Mol: CCC>
>>> data = [m, skchem.Mol.from_smiles('C=CO'), skchem.Mol.from_smiles('C[O-]')]
>>> std.transform(data)
0 <Mol: CCC>
1 <Mol: CC=O>
2 <Mol: CO>
Name: structure, dtype: object
>>> will_fail = mol = '''932-97-8
... RDKit 3D
...
... 9 9 0 0 0 0 0 0 0 0999 V2000
... -0.9646 0.0000 0.0032 C 0 0 0 0 0 0 0 0 0 0 0 0
... -0.2894 -1.2163 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0
... -0.2894 1.2163 0.0025 C 0 0 0 0 0 0 0 0 0 0 0 0
... -2.2146 0.0000 -0.0004 N 0 0 0 0 0 0 0 0 0 0 0 0
... 1.0710 -1.2610 0.0002 C 0 0 0 0 0 0 0 0 0 0 0 0
... 1.0710 1.2610 0.0007 C 0 0 0 0 0 0 0 0 0 0 0 0
... -3.3386 0.0000 -0.0037 N 0 0 0 0 0 0 0 0 0 0 0 0
... 1.8248 0.0000 -0.0005 C 0 0 0 0 0 0 0 0 0 0 0 0
... 3.0435 0.0000 -0.0026 O 0 0 0 0 0 0 0 0 0 0 0 0
... 1 2 1 0
... 1 3 1 0
... 1 4 2 3
... 2 5 2 0
... 3 6 2 0
... 4 7 2 0
... 5 8 1 0
... 8 9 2 0
... 6 8 1 0
... M CHG 2 4 1 7 -1
... M END
... '''
>>> will_fail = skchem.Mol.from_molblock(will_fail)
>>> std.transform(will_fail)
nan
>>> data = [will_fail] + data
>>> std.transform(data)
0 None
1 <Mol: CCC>
2 <Mol: CC=O>
3 <Mol: CO>
Name: structure, dtype: object
>>> std.transform_filter(data)
1 <Mol: CCC>
2 <Mol: CC=O>
3 <Mol: CO>
Name: structure, dtype: object
>>> std.keep_failed = True
>>> std.transform(data)
0 <Mol: [N-]=[N+]=C1C=CC(=O)C=C1>
1 <Mol: CCC>
2 <Mol: CC=O>
3 <Mol: CO>
Name: structure, dtype: object
DEFAULT_CONFIG = '/home/docs/checkouts/readthedocs.org/user_builds/scikit-chem/checkouts/latest/skchem/standardizers/default_config.xml'¶columns¶install_hint = ' Install ChemAxon from https://www.chemaxon.com. It requires a license,\n which can be freely obtained for academics. '¶